Molecular Dynamics Siumlations with Gromacs

Aleksandar Mehandzhiyski
Virtual Simulation Lab seminar series
www.virtualsiml...

[@MsSADAFRANI]

Thank you for such a nice presentation. I was trying MD which was seemingly difficult for me. After seeing this presentation I got a lot of understanding. thank you so much

[@nelsonbarrios1718]

Thanks a lot for this excellent presentation 👍👍 It helped me to understand more about GROMACS

[@aleksandarmehandzhiyski2964]

Great, I am glad it was helpful. :)

[@mzheleva]

Супер! Лекцията беше много полезна за изпълнението на моята първа симулация с GROMACS!

[@aleksandarmehandzhiyski2964]

Радвам се че видеото е било полезно за вас.

[@sekekeretsu4172]

YOU MADE IT LOOK SO EASY. PLEASE UPLOAD MORE OF YOUR WORKS .

[@placidoism]

Hi Aleksandar, thanks a lot for your tutorial but a I have a big doubt. How have you created the file topol.top? You don't write any output comand with -o topol.top and suddendly you use it when solvate molecules. I am having a lot of problems with topology, a little help will be welcome. Thanks :D

[@luiscarlosperez7426]

same problem. Have you done yet ?

[@explorewithashokgunturu]

I got the same problem while performing the simulation. After that, I saw couple of sample .top files and wrote one my own. I believe, the topol.top file has to be written by the person who performs the experiment.

[@explorewithashokgunturu]

You can see the contents of topol.top file that has been used by him at 31:34. Just create a file with the name topol.top and write the displayed content on the file.

[@ZohanSyahFatomi]

Nice tutorial, however if there is a subtitle in english that will be more much appreciated. :D

[@gabco11]

Great tutorial, thanks a lot !

[@juliopdaniel]

Greetings from Brazil! I would like to see something about comparative modelling (i´m a begginer in computational biology). Thanks a lot for this presetantion!

[@matchem9178]

Thanks!

[@EwelinaRutkowska]

Thank you for uploading this seminar. It is very helpful. Is there any repository from where the files of this trial can be downloaded?

[@VirtualSimulationLab]

You can find all the materials on our webpage www.virtualsimlab.com

[@EwelinaRutkowska]

Precisely: www.virtualsimlab.com/archive/ Thank you!

[@ranam]

Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products

[@klusblody]

Gromacs for the win

[@alejouchihasama]

good video, however I am doing it to the letter and an error appears when adding the ions, it says that there is an error in the recognition of the atoms ... for help. Thank you

[@tannguyen1292]

thanks you so much. Could we use one topol.top file for all molecule? or we must create a new topol.top for every molecule. Thanks

[@farzanehahmadi1171]

why I can’t produce mdp format in gromax? in all my reserch, see downlod links of ions. mdp for lyzozim. but i want produce that is or find mdp format for every protein. please, help me. thank you so much.

[@rajendrakc5969]

I don't know about producing, but you can definitely edit those MDP files as per your need

[@sajadyaghoubizadeh8416]

Hi guys, is it possible to simulate the bioabsorption process by GROMACS or any other MDS apps? it's necessary. Thx

[@truongtonchu]

Can you show how to simulation CO2 with amine or ILs? Thank you

[@wenchongzhou2601]

Why we have to adjust the order of atom coordinates at 23.05? Can anyone please tell me, many thanks!

[@19neetish]

because charges were wrong. The script only predicts the type of atom and in the case prediction was wrong.

[@rangkhuray2305]

i running umbrella sampling. but i don't have file complex.gro. how i can get the file? thank you for your answer,.

[@zoizwitsa9627]

you can search in this site for configuration atb.uq.edu.au/index.py and then use editconf in gromacs to produce your complex.gro file

[@AliceFan-je1dm]

senior intellectuals

[@nijatshukurov9022]

I cant find topolgen file.

[@PharmaAI-LearningCenter]

Please guide me on how to run MD on gromacs with GPU. Running MD on GPU showing error

[@susmitaroy3899]

You may use command (-nb gpu) for example gmx mdrun - v - deffnm em - nb gpu I hope it helps...

[@AxlSPPDgame]

So, the link page doesnt work anymore??

[@aleksandarmehandzhiyski2964]

It does not work at the moment. The page is supposed to be updated.

[@RakeshBhowmick]

Can I run a simulation of 50k atom in my desktop pc having i5 processor for 20ns

[@markjack686]

Yes, you can. but I think you will cost a few days for running if you have not use GPU acceleration.

[@asmauhamza288]

Please what is GPU acceleration

[@asmauhamza288]

Please what is GPU acceleration

[@sangeetakhargharia8752]

Can someone suggest me some papers on which these types of works are done..

[@aleksandarmehandzhiyski2964]

www.tandfonline.com/doi/full/10.1080/00268976.2016.1155776

[@sangeetakhargharia8752]

@@aleksandarmehandzhiyski2964 thank u 😊

[@sangeetakhargharia8752]

is there any supporting information in this paper i couldn't found it?

[@aleksandarmehandzhiyski2964]

No, there is no SI.

[@umakantapradhan1327]

hiiiii thnx for the tutorial. I am beginner to GROMACS. I was unable to understand how u got the all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top. Please help!!!!!!!

[@aleksandarmehandzhiyski2964]

Hi, all of these files are simple text files, which I have created some time ago, and just reuse/modify whenever I need them. You can find the files used in the presentation in the Virtual Sim Lab webpage.

[@umakantapradhan1327]

@@aleksandarmehandzhiyski2964.... can u teach me how can i generate or create all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top for my molecule.

[@umakantapradhan1327]

@@aleksandarmehandzhiyski2964 sir I am still waiting for your reply. Can I have your email id for better communication about GROMACS.

[@computational_biophysics]

Greetings sir, where can i download this presentation?

[@manueliny1990]

What is science? 😕